Bandicoots and bilbies (order Peramelemorphia) represent the principal group of omnivorous marsupials from a range of habitats across Australia and New Guinea. Bandicoots and bilbies most commonly use quadrupedal, asymmetrical half-bounding or bounding gaits and present an unusual combination of hind limb morphological features, including an ossified patella, a modified tibiofibular joint, and syndactylous morphology of the pes. We performed comparative dissections of the hind limb of the southern brown bandicoot (Isoodon obesulus fusciventer) (n = 13) and greater bilby (Macrotis lagotis) (n = 4), providing detailed descriptions of the muscular anatomy. These species displayed significant modification of the hind limb muscular anatomy and associated connective tissues, including emphasis on multiarticular muscles, such as the hamstrings, and extreme development of fascial structures. These patterns were more extreme in I. obesulus than in M. lagotis. Differences between the hind limb anatomy of I. obesulus and M. lagotis reflect the different ecological and environmental pressures on their locomotion and digging behaviours.